Dear gmx-users, I'm running my simulations on a machine with a queue system that stops the runs longer than 24 hours. Often, for my simulations, I need a longer time to complete the runs. Let's have an example. I have to run a 100ns-long simulation on a machine that produces 10ns/days simulation. I have two possibilities: First approach: I'm setting within the .mdp file a global duration of 100 ns. Then: grompp -f param.mdp -c prot.gro -p topol.top -o input_fullMD.tpr mdrun -s input_fullMD.tpr -deffnm output_fullMD After 24 h, I see that the run has been stopped after 10 ns. I have the output_fullMD.cpt file. Then, I do: mdrun -s input_fullMD.tpr -cpi output_fullMD.cpt -deffnm output_fullMD_2 and so on for 10 days, until the run has been completed (then I will concatenate the .xtc, .edr, .trr files) Second approach: I'm setting within the .mdp file a global duration of 10 ns. Then (as above): grompp -f param.mdp -c prot.gro -p topol.top -o input_fullMD.tpr mdrun -s input_fullMD.tpr -deffnm output_fullMD After 24 h, the run has been finished. Then, I continue the run for other 10 ns with: tpbconv -s input_fullMD.tpr -extend 10000 -o input_fullMD_2.tpr mdrun -s input_fullMD_2.tpr -cpi output_fullMD.cpt -deffnm output_fullMD_2 and so on for 10 days, until the 100-ns run has been completed. Are the two procedure producing EXACTLY the same results, or not? Which is the best preferred procedure? Thank you very much Anna ____________________________________________________ Anna Marabotti, Ph.D. Web page: http://bioinformatica.isa.cnr.it/anna/anna.htm "When a man with a gun meets a man with a pen, the man with a gun is a dead man" (Roberto Benigni, about Roberto Saviano)
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